From 294bf107faeda94dc2e00e307eff982b18b6da67 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 18 Jan 2024 18:03:21 +0000
Subject: [PATCH] fix(metadata): compare dataframe with None
find_channels_per_position compares dataframe with None to check data exists
---
src/agora/io/metadata.py | 2 +-
src/aliby/pipeline.py | 9 +++++----
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/agora/io/metadata.py b/src/agora/io/metadata.py
index 44e3d70..4da1b28 100644
--- a/src/agora/io/metadata.py
+++ b/src/agora/io/metadata.py
@@ -155,7 +155,7 @@ def find_channels_by_position(meta):
channels_dict = {group: [] for group in meta.index}
for group in channels_dict:
for channel in imaging_channels:
- if meta.loc[group, channel]:
+ if meta.loc[group, channel] is not None:
channels_dict[group].append(channel)
elif isinstance(meta, dict):
channels_dict = {
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 686bd15..2b96210 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -300,14 +300,15 @@ class Pipeline(ProcessABC):
"""Run separate pipelines for all positions in an experiment."""
# display configuration
config = self.parameters.to_dict()
- for step in config:
- print("\n---\n" + step + "\n---")
- pprint(config[step])
- print()
+ print("\nalibylite\n")
try:
logging.getLogger("aliby").info(f"Using Baby {baby.__version__}.")
except AttributeError:
logging.getLogger("aliby").info("Using original Baby.")
+ for step in config:
+ print("\n---\n" + step + "\n---")
+ pprint(config[step])
+ print()
# extract from configuration
expt_id = config["general"]["id"]
distributed = config["general"]["distributed"]
--
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